The overall goal of phase I and II of this proposal is to develop microarray-based methods for high throughput profiling of proteins. This will be done in two different ways, one based on arrays of 100s of thousands of distinct peptides on 1 cm2 chips that can be used to fingerprint proteins, the other based on thousands or tens of thousands of antibodies against proteins, given only the genomic sequence of the proteins. Both methods require a fabricator for producing high density peptide arrays inexpensively and rapidly. In particular, phase I has the following aims: 1. Synthesize photolabile- amino acids 2. Attach photolabile amino acids to amino-glass slide. 3. Determine optimum deprotection time and appropriate solvent conditions. Improve the yield per step of amino acid coupling. 4. Synthesize peptide arrays. 5. Demonstrate the systems on a small scale for known peptide protein interactions, establishing signal reproducibility and response characteristics. 6. Develop in silico methods to effectively select millions of different peptide sequences such that tens of different sequences will bind virtually any protein presented to the array.